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Fold and Unfold

Animation of GFP unfolding

For the most part of biology, it is form that follows function. Proteins are a perfect example of this -- they are made of a sequence of amino acids (the protein building units), which are synthesized by the ribosome. Once synthesized, the long strings of amino acids fold up into a particular 3D shape or conformational state. Proteins take less than a thousandth of a second to attain their preferred conformational state (called “native state”) that -- if nothing goes wrong -- ends up being the same for a given sequence. This process is called protein folding. Explaining how a protein finds its folding preference out of all possible ways in such a short time is a longstanding problem in biology.

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Tiny Tubes Racing in a Donut-Shaped Track

The shape of a container can affect the flow of the fluid inside it. Water in a narrow stream flows smoothly, but once the water molecules make their way into a pond, they spread out and no longer flow coherently. If you blow into a long, narrow straw, the air will go straight through. Once the air flows into the large room you are standing in, it slows down as it mixes with the air around it, so someone standing five feet away from you won’t feel a breeze at all.

The above examples show how the shape of a container affect the flow of passive fluids. In today’s study, Kun-Ta Wu and colleagues investigated how the motion of active fluids, fluids that flow using an internal source of energy, is also affected by the shape of their container. They used a system of microtubules, chains of proteins assembled into long, stiff rods. Clusters of a protein called kinesin exert a force on microtubules by “walking” along them. Microtubules interact with each other to form swarms or turbulent-like flows.

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Self-assembling silk lasers

Rings, spheres, and optical resonators self-assembled out of silk

When I first learned about the coffee ring effect I thought it was super cool, but it seemed like an open-and-shut case. Why do rings form where some liquids, like spilled coffee, are left to dry? Roughness on the table causes the liquid to spread imperfectly across the surface, pinning the edges of the droplet in place with a fixed diameter. Because the diameter of the droplet can’t change during evaporation, new liquid must flow from the droplet’s center to the edges. This flow also pushes dissolved coffee particles to the edges of the droplet, where they are left behind to form a ring as the water evaporates away (Figure 1). More details can be found in our previous post, here. It’s a complicated phenomenon, but after being described in 1997 it doesn’t seem like anything new would be going on here. Right? Well, as it usually happens in science, classic concepts have a way of popping back up in unexpected ways. Last year Itır Bakış Doğru and her colleagues in Prof. Nizamoğlu’s group at Koç University, Turkey published a study using the often troublesome coffee ring effect to their advantage: making self-assembling silk lasers.